Touch screen has dead spots and other weird stuff

I have researched this issue and read that it has to be replaced. I unrooted and returned to stock and recieved the latest OTA. My question is the root apps, like CLockwork, setcp etc still show in market but are not installed. Is that going to be a problem?

Also, where my droid is 1 year and 4 months old, will they replace it with a refurb? It is in perfect condition with almost no screen blemishes if it matters. I can upgrade but holding off for thunderbolt.